The Manhattan Project
by lilmickey2008
Summary: Miley Stewart is in for a big surprise when she and her friend Michael head out to New York for a concert. Not only do they encounter the TMNT, but the Foot, Shredder and Kraang are going to get involved.
1. A Foot in SeaView

**AN: Well, this is my newest attempt at a TMNT/Hannah Montana story. It came to me as I was watching the newest episode of the current incarnation of this franchise. I hope that you will enjoy it as much as I did writing it.**

**Chapter One: A Foot in Seaview **

Michael Harris for all intent and purposes, was not a normal teenager. Then again, in this day and age, who was? He had friends, family, and like all teenagers, a secret that he wanted to keep from everyone he cared about because it was life and death. Really, it was. All she knew about him was that he grew up in the west. First, he was born in Manhattan, New York, and then he lived out in Missouri, Saint Louis to be exact. As to why he left New York, that was really a grey area. He did not want to talk about it, and his friends never really pressed that issue. Miley Stewart knew that he was hiding something, and although she really want to find out just what he was hiding from her, she knew that she had to be careful about finding out what his secret was, or she was going to lose one of her closest friends. This was not going to be easy, that was for sure.

* * *

><p>At school the next day, he had the strangest feeling. It was almost like someone was watching him. He could not shake it, and if he tried, the feeling would grow stronger. That was never a good thing. He sighed, and tried to get through the school day. He should like school, and he was smart enough, but school was boring, even to the smart kids.<p>

As he was at his locker, getting his books, he felt those mysterious eyes from the shadows watching him again. He wasn't getting scared, though, but he was now starting to get a little pissed off.

"Whatever is watching me, if you don't do something soon, I am really going to get mad and violent." Michael told himself. "If you have the balls, show yourself."

Wish granted.

Michael turned a corner down a hallway, and what was he greeted with?

Footbots. Three footbots.

"Footbots? What the hell were they doing here in California?" Michael asked himself. Michael dropped his books, and ran back around the corner to his locker. He was digging inside of the locker when the footbots were rounding the corner and coming right at him while he was doing that. They launched themselves at Michael, and just as they were about to strike him, Michael impaled one of the impending footbots, right through the head with one of the swords he had hidden in his locker for just this occasion, destroying one of them. As the two remaining footbots began to try and run away, Michael threw his other sword, impaling the other robot, destroying that one as well.

The third footbot thought that it was in the clear, when Michael appeared out of nowhere, cutting it in half. Once he put down the third footbot, he knew that he was in the clear, for now anyway.

"Just what in the hell were these things doing in Malibu, anyway?" Michael asked himself. He had to get some answers, and Michael knew just exactly where to get those answers.

* * *

><p>It was a sunny Tuesday afternoon, the same afternoon that he was attacked by the footbots, and Michael quietly sat at his desk. What he was going to do was log on to face chat with his friends back home in New York. He patched in his password, and sat patiently as his computer came up to face chat. That meant that the connection was good, and he was going to face chat with someone he has not seen in a while.<p>

"Hello?" A red headed girl a little younger than him said.

"April? It's me, Michael." Michael said, waving.

"Oh, hey Michael!" April said in a cheerful tone. "How are things in Malibu?"

"That's why I am calling." Michael said. "Are any of the turtles around?"

"Sure." April said. She knew that tone all too well. Whatever he said, it was not going to be good news. April sat down the computer, and off screen, Michael could hear her call for her friends. Soon enough, one turtle with a blue headband appeared on April's computer.

"Hey Mike, what's up?" Leonardo, the leader, said to him.

"I have a problem, the Footbots attacked me at school today." Michael said.

"What!? How were they able to get out there to California?" Leo asked.

"The Kraang transported them out here, best guess." Michael answered.

"What did you do to them?" Leo asked.

"I disposed of them." Michael answered. "Out of sight, of course."

"Listen, we would come out there to investigate..." Leo tried to say, but Michael cut him off.

"Don't bother." Michael said quickly. "More likely than not, whatever he has planning is going to be out of New York City."

"And by 'he' you mean Shredder." Leo said.

"Yeah." Michael agreed. "Listen. Keep an eye out up there, okay?"

"Yeah, same to you." Leo said.

* * *

><p>Michael was at his desk reading when he got a knock on his door. He opened it to see his friend from school, Miley Stewart. She smiled, and walked inside. She strolled over to his bed, and sat down.<p>

"Michael, I have a really big favor." Miley said.

"Okay, what's up?" Michael asked her.

"I have a performance in New York next week, and I really want to go, but dad won't let me go." Miley said in a sad tone.

"There is a but, right?" Michael asked.

"I can go, but not unless I have you come with me." Miley said looking up at him with those beautiful blue eyes of hers.

"So, you want me to go with you to New York, and you cannot go unless I go, right?" Michael asked her, just to make sure he has this straight and right.

"Right." Miley said.

Michael thought for a few moments, and sat next to her.

"Fine. I'll go with you." Michael said with a smile.

"Thank you." Miley said, giving him a kiss on the cheek. "I'll call you with the details."

"Okay." Michael said. He could only smile as he watched her leave. His smile drained as he knew who was waiting in New York for him.

Shredder, and the Foot...

* * *

><p><strong>AN: Next chapter, Michael and Miley arrive in New York, and while Miley is off doing her business, Michael looks up some old friends. Thanks for reading and keep an eye out to see what happens next!<strong>


	2. Reunited

**AN: As stated last chapter, if I didn't state it or make it clear, sorry in advance, Miley and Michael arrive in New York. While Miley does business, Michael goes and meets some friends, or rather family if you think about it.**

**Chapter Two: Reunited**

It was like the calm before the storm, but let's be honest here, that is exactly what it was. A calm plane ride couldn't keep the thought that he was returning to the past away from him at all. He knew that the Foot and of course Shredder were going to be aware the moment that he would touch down, and he knew that all too well. That was one problem, the second being the Kraang. Michael knew that he had to deal with them as well. As he sat in his seat, Michael soon came to the realization that it was not all bad coming here. He had family, not blood family, but family none the less.

It was going to be good seeing Master Splinter, April, Casey, and especially the four Turtles. He was going to surprise them all, because they would not know that he is going to be here, and they will once things start to pick up, whatever that may mean.

* * *

><p>It was late in the evening, but not quite nighttime, when they arrived in New York City. The cab ride to their hotel was just as quiet as the plane ride to the city itself. After checking into the hotel, and ignoring the look Michael got from the lady that checked them in, Miley dragged her friend to the room that was theirs. They opened the door, and got a look at their room. The room had a really big dresser for their clothes, two lamps on each side of the single bed in the room, and at the end of the somewhat hall in the room, there was a mirror with racks for the towels and their bathing products.<p>

Michael placed his suitcase at the door, and sat himself on the bed. Miley did the same, and sat next to her friend.

"Well, that was easy enough." Michael said, laying back on the bed.

"Yeah, it was easy." Miley said sitting next to her friend. "So, what do you want to do now?"

"Well, there is a pizza restaurant next to our hotel. Want to head there in a few hours and get some dinner?" Michael asked her.

"What is with you and pizza?" Miley laughed. "I have never seen you without some type of pizza in your mouth."

"Hey, when I lived out here, that is all I ate." Michael said. "I know where the best pizza is, but it is a bit of a ways out there."

"Fine. Let's go right now." Miley said, all but yanking him out of the door of their hotel room.

* * *

><p>It was around nighttime, and Michael and Miley were busy walking through the streets of New York. It was a fairly quiet, somewhat cool, and clear night. They were heading towards the restaurant that Michael mentioned before, and Miley went along with where they were going. Miley thought that New York was fairly quiet, but Michael knew that around this time at night, his four friends are usually running the rooftops, doing god knows what.<p>

Speaking of Michael's four friends, as they rounded a corner, Miley took a look up towards the star ridden sky, and saw something running on the roofs of buildings in front of them. Whatever it was, it was not alone, as well as she could see in the dark, she saw that there was at least four of whatever it was.

"Michael!" Miley said, grabbing his arm, and forcing him to stop.

"What, what is it?" Michael asked her.

"I saw something! Something on the roofs!" Miley said, pointing to the building in front of them. Michael looked to where she was pointing, and saw that whatever she did or did not see, was long gone by now.

"I don't see anything. You must be imagining things." Michael said.

"No, I really saw something." Miley said. Michael knew she was telling the truth, but he did not play along.

"Really? How many of this 'thing' did you see?" Michael asked her.

"At least four." Miley answered. Michael knew immediately what she saw.

_The Turtles. She saw the Turtles._ Michael thought. Unfortunately for him, Miley picked up on this, and looked him in the eye.

"Oh! So you know what I saw!" Miley all but screamed at him. "What was it?"

Also bad, he was a very bad liar, especially to Miley.

"I don't know." Michael said in a very bad tone of voice.

"Sure. I am going to find out, and you are going to tell me, even if I have to make you." Miley said, walking ahead of him.

"Great, freaking great." Michael sighed, running ahead to catch up to her.

* * *

><p>It was about nighttime, and Miley was asleep in their room. Michael awoke at about midnight, and for some reason, and he quietly slid his St. Louis Rams hoodie, and made his way towards the soda machine nearby. He was there by himself when he felt a presence soon nearby. He let out an irritable sigh when he heard someone come up from behind him.<p>

"She saw you, you know." Michael said. He turned around to see Leonardo, Donatello, Michaelangelo, and Raphael standing in front of him.

"Yeah, sorry about that." Leo said, rubbing the back of his head. "More importantly, what about the Footbots that attacked you at school?"

"Yeah, it was weird." Michael began. "I was at my locker, and when I rounded a corner, I saw three footbots. They tried to attack me, but I put them down before they could do any damage."

"Wow, really? How did they get there in California?" Donnie asked.

"A portal from the Kraang, most likely." Michael answered.

"There's no way that the Foot are just attacking you for no reason." Raph said. "Do you think that Shredder knows you are back in New York?"

"No doubt." Michael answered. "Wait, how did you guys find me here?"

"Honestly? We tailed you from the pizza place." Leo said.

"Speaking of pizza, who was the chick that you were with?" Mikey asked him.

"A friend." Michael said.

"Are you gonna bring her around the lair?" Mikey asked.

"Yeah, I am going to bring her around four mutated turtles, a mutated rat, in a sewer." Michael said sarcastically.

"Really? When?" Mikey asked innocently.

"I was being sarcastic, Mikey." Michael said.

"Is that her?" Donnie asked, pointing up towards the hotel room that he shared with Miley. The five of them looked up to see Miley looking around for Michael, and when he looked down in their direction, they were able to hide out of her sight just in time.

"Dude, this is nuts. Why don't we just go and say hi to her?" Mikey asked.

"Wow, you really don't get it, do you?" Michael asked him. "She doesn't know about you guys, and until I absolutely have to, I am not going to say anything about you guys."

"Fine with me." Leo said. "Tomorrow, come to the lair when you get the chance."

Alright, see ya." Michael said. He watched as his friends disappeared into the darkness. Michael quietly made his way back to the hotel room, feeling glad that at least he got to see his friends.

* * *

><p>Once Michael got back to the hotel room, Miley was already in bed, sound asleep. He quietly changed into his pajamas and slid into bed beside his friend. While it was good to see his friends again, he could not help but feel that a showdown with the Foot was coming up. If he was going to find the foot, he knew that he was going to have some help with the Turtles.<p>

With that helpful thought in his mind, he closed his eye, and drifted off to sleep.

* * *

><p><strong>AN: Well int the next chapter, while Miley goes about her business, Michael reunites with Master Splinter, Casey, and April. That's good. The Foot trying to get to Miley, that's bad...<strong>


	3. Quality Time

**AN: Well, not only will Michael have some quality time with the Turtles and Master Splinter, but some quality time with Footbots as well. Go figure.**

**Chapter Three: Quality Time**

Michael was damn sure now that Miley knew that he was hiding something from her. Last night, Michael had a conversation with Leo, Mikey, Raph and Donnie, but barely got clear before Miley caught them talking. He knew that Miley knew that he was talking to someone, but she did not see him talking to someone. The next morning, Miley did not say anything about the night before, him talking to someone that she could not see. He wondered how long it was going to be before he got caught talking to the Turtles. It was going to happen, and Michael was willing to bet everything that he owned that it was going to be before they headed back to California. Well, no use in worrying about that now, right?

* * *

><p>He had a lot of free time to himself, all the while Miley had soundcheck, and various stuff to do before she headed to do an interview, so that meant that Michael was going to be all by himself for a while. So what did he do? He went to school. Casey's and April's school to be precise. Michael checked his clock, and it showed that it was about time for them to head home. Just as he arrived at their school he saw them walking away and decided to catch up to them.<p>

"Hey Casey! April!" Michael said, running up to his friends. They turned around and smiled, while waving him over.

"Hey man, what are you doing here in New York?" Casey asked him.

"A friend of mine had a musical performance, and I had to come with her." Michael answered.

"So, what are you doing right now?" April asked him.

"Honestly? Nothing, just hanging around, trying to keep busy until Miley is done with her business." Michael said, taking a deep breath.

"Hey, you coming to the lair later?" Casey asked him.

"I might." Michael answered. "The thing is, Miley does not know about the Turtles, or Master Splinter."

"Not to mention the Kraang and the Foot running around here." April said.

"If all things go well, I should be at the lair tonight, definately." Michael said in a hopeful tone.

"Alright, see you then." Casey said. The three friends said their goodbyes, and went on in their separate ways.

* * *

><p>Michael somehow wandered back to the area where Miley was practicing, and the moment he saw that building where she was supposed to be, he got a really bad feeling. Michael scanned the area, and saw a small group of five footbots lurking around the building.<p>

_Crap, these clowns again. _Michael thought to himself. He got out his shellphone, and quickly texted the Turtles.

"Great, this is going to be fun." Michael said. He quickly ran after the footbots to see where they were going.

* * *

><p>The footbots began to slowly creep around the building, just looking for someone. Michael knew they were after either Miley or himself, so he had to be sure that they would not get their hands on her. Michael saw them, and a smile slowly crossed his face. He smiled because he had a surprise for these tin jerks.<p>

"Well, you guys are looking for another bruising, huh?" Michael said, loudly enough to get their attention. They turned all at once, and saw him. The footbots got armed, and began to pursue him outside.

"Now guys!" Michael screamed. The footbots looked up, and that is when Leo, Raph, Donnie, and Mikey came from above, and struck them down in one well aimed swoop. Once that was done, the five friends came together.

"Thanks guys." Michael said with a sigh.

"This is kind of ridicilous. Why would Shredder send only five footbots to kidnap you?" Leo asked.

"Most likely, they were after Miley. We just foiled their plans." Michael answered.

"Wait, why would the Shredder be after some random chick he never met?" Raph asked.

"To get to me, most likely." Michael said.

"Sounds about right. It would not be the first time that Shredder pulled something like this." Donnie said.

"Dudes, this is really getting out of control. What is going to happen next?" Mikey asked.

"I honestly have no clue." Michael said.

* * *

><p>Michael managed to get back to the studio just in time to see Miley before she was done with her business. Michael was waiting in her when she walked out, and then she looked at him with a smile on her face.<p>

"Well, it's nice to see you here." Miley said. "Where have you been?"

"I kind of figured that you were going to take a little while, so I went to see some of my friends." Michael said, truthfully.

"Really? What type of friends are you talking about?" Miley asked him.

"Somewhat normal friends." Michael said.

"Okay. I hope I get to meet these friends of yours sometime." Miley said.

"Don't worry. You will get to meet these friends of mine soon enough." Michael said, giving her a smile.

* * *

><p><strong>AN: Well, in the next chapter, Miley will get her wish, and boy will she ever get it...<strong>


	4. Secrets of the Ooze Revealed

**AN: Well, as Michael and the Turtles continue their activities. When Miley gets suspicious, she decides to follow Michael and finally sees where he is really going. This chapter is partly inspired by the second live action movie, **_**Teenage Mutant Ninja Turtles 2: Secret of the Ooze**_**. Not a lot, but enough that it warranted that credit.**

**Chapter Four: Secrets of the Ooze Revealed**

He hated this.

Michael hated keeping a secret from Miley, and it was damn obvious that she knew that he was keeping something from her. He really wanted to tell her what he was hiding, but he did not know how she was going to take it, so he was apprehensive about telling Miley about his friendship with the Turtles, and especially Master Splinter. He just sighed, and kept walking towards his destination. He just wondered what was going to happen in the near future. It was not going to be good, he sort of knew that. Shredder probably knew that he was here, and he could not stop thinking about it.

There was a showdown coming, and it was coming really soon.

* * *

><p>For some reason, strange enough, Michael considered Master Splinter to be his father, or at the very least, a father figure. Master Splinter always gave him sage like advice when he originally lived there, and on the rare occasion, he saw him actually fight, and no one, including Shredder, would never be able to take him.<p>

Michael was on his own, wandering the streets as a young child when Master Splinter found him. Michael stayed with Master Splinter until he could find out about his other family in California, and when he did, Master Splinter made the decision to send Michael out there to live with his biological family. Michael vowed that when he was older, he was going to come back to see the four Turtles, and of course, Master Splinter.

Now he has kept that promise, but there still was some unfinished business to take care of.

* * *

><p>Michael was again walking around the town, just trying to keep himself busy. He let Miley go around to do her own thing, and Michael began to basically walk around town again, looking for something to do. He soon found himself wandering down a sewers, and heading towards the Turtles lair. Walking through the sewers, he soon reached the lair. The Turtles were there, Leo, Raph, and Mikey were watching TV. Donnie was probably in his lab, doing something, or rather working on a project of his.<p>

"Hey guys." Michael said, getting their attention.

"Hey, Michael, what brings you around our way?" Leo asked him.

"I had some time to kill, so I figured that I should see what you guys were up to." Michael said, taking a seat next to Mikey.

"Nothing really." Raph said. "When we are not busting heads, we are more than likely hanging out down here."

"Michael, there was something that I meant to ask you." Leo said. "How did Master Splinter managed to find you?"

"I was wondering the streets after my mom died." Michael said sadly.

"Really? How did that happen?" Raph asked.

"My father sold her out to the Foot Clan." Michael said.

"Wow, that sucks." Mikey said.

"To make it worse, it was for money that he did it. Not even a lot of money either." Michael said.

"Yeah. There are guys like that in this world." Leo said.

"Is Master Splinter in? I wanted to talk to him before I left." Michael said, quickly changing the subject.

Leo pointed in a certain direction, and Michael followed where the blue clad turtle pointed.

"Thanks." Michael said.

* * *

><p>"Hello, Michael." Master Splinter said, seeing Michael.<p>

"Hey, Master Splinter, I wanted to talk to you real quick before I left." Michael said.

"Fine. What about?" Master Splinter asked him.

"Things. Ever since I came back, something has been bothering me." Michael said. "I needed to know, why did you take care of me after you found me?"

Master Splinter was silent for a few moments, obviously deep in thought. Then he spoke up.

"I always had a thing for helping others in need." Master Splinter said. "That is one thing I have always kept with me from my human form."

"I know that before I leave New York that I am going to confront the Shredder and the Foot. I wonder if I would be ready for it." Michael said.

Master Splinter placed his hand on Michael's shoulder. "You will be ready when the time comes."

"You are a way better man than I am, and you aren't even a full human." Michael said, laughing.

Master Splinter shared a soft laugh as well, knowing that Michael meant well.

"Thanks, Master Splinter. I hope to see you again before I leave." Michael said, heading for the exit.

"Farewell, my son." Master Splinter said.

* * *

><p>It was late into the next day, and Miley was busy doing her own thing once again, and Michael was out walking the city again, or so he said. Miley then decided to skirt on her own duties, and follow her friend to see what he was really doing. She noticed that he was standing there, talking to a red head about her age, and she grew increasingly jealous.<p>

"So, you were hanging around some girl, huh?" Miley said, an angry smile on her face. Once Michael and this girl walked off, Miley decided to follow them to see where they were going.

"Now I am going to find out just what you are really doing, Michael." Miley said, smile on her face.

* * *

><p>It was the rare occasion that the four Turtles were all out, and at April's place. April invited the four of them out to her house, and it was Michael that walked her there. It was good and fun to have all of his friends there, and Michael was having a good time there.<p>

"Hey, Leo, is it alright with Master Splinter that you guys are here?" Michael asked him.

"Sure." Leo said. "We stick to the shadows, and made sure that we were not followed."

"Yeah, besides, it would do us some good to get out of the sewers and walk around on the surface once in a while." Raph said.

"Aren't you worried that something bad might happen?" Michael asked the Turtles.

"It's not as if we can't handle ourselves." Donnie answered from across the room.

"Yeah, what's the worse thing that can happen?" Leo asked, laughing as well. "Miley is gonna find us?"

**BOOM-BOOM-BOOM.**

All five of them flinched as the hard knocking came loudly, echoing throughout the house.

"Crap, who's that supposed to be?" Leo asked.

**BOOM-BOOM-BOOM. ** The knocking came again, even louder this time.

"Whoever that is, they are not going away." April said.

"Who could that be?" Leo asked.

_Please be the Foot. _Michael thought.

"Michael! It's me, Miley! I know you are in there! Open the door!" Miley screamed.

"Crap." Michael thought.

"Dude, your girlfriend followed you?" Raph said.

"She's not my girlfriend, meathead." Michael shot at Raph.

"Great, now what are we going to do?" April asked him.

"Hide!" Michael said to the Turtles. Leo and Donnie ran into a bedroom, and Raph hid in a nearby closet. Once they were all hid, Michael opened the door, to an angry Miley.

"Hi." Michael said, not knowing how angry she was. Miley shoved passed him, and looked around. Then she saw April, and sighed.

"Who were you talking to?" Miley asked him.

"This is April by the way." Michael said, pointing to April.

"Hi, who were you talking to?" Miley asked him.

"I was talking to April." Michael said, techincally telling the truth.

"I heard you talking to some guys in here." Miley said, looking around the apartment. "Now they are gone. Am I going to have to look around until I see something?"

"Wow, jealous much?" April asked her. Miley shot a look at April, and before anything can happen, he stepped in between them.

"Look, I'll explain everything back at our room, okay?" Michael said. He moved Miley to the door, and Miley was about to leave when she saw something sticking out from the closet door.

"Really? No one is here, huh?" Miley said. She walked over to the closet door, and smiled slyly.

"Explain this!" Miley said, stomping down hard on Raph's foot.

Raph screamed out in pain, falling out of the closet as he did so. Raph grabbed one of his si's and pointed it directly at Miley.

"Oh, you are gonna pay for that!" Raph said, moving towards her as April and Michael struggled to hold him back. Miley fell on her butt, backing away from him in mortal fear.

"Raph, calm down!" Michael said, struggling to hold him back. "Guys! A little help here!"

Miley watched as two more of these things came out, one wearing blue, and the other wearing purple, and held back the one in red. While Donnie and Leo helped to calm down Raph, Michael tried to calm down Miley.

"Miley? Miley, listen to me-" Michael began, and just as things were calming down a little...

"Hey! Michael's girlfriend? I'm Mikey!" Michaelangelo said, a slice of pizza hanging from his mouth.

The sight of four mutant turtles appeared to be too much for Miley. Michael noticed that she appeared to be uneasy on her feet, and soon enough, Miley fainted.

"Was is something I said?" Mikey asked innocently.

* * *

><p><strong>AN: Coming up, Michael comes clean to Miley about everything, and she gets another big surprise. Thanks for reading, and stay tuned for more!<strong>


	5. His Unconventional Family

**AN: Well, last time, Miley got a very, very big surprise from her friend, Michael. She finally met the friends that he has been sneaking off to meet. Of course, Miley gets another surprise, and will it be a good one?**

**Chapter Five: His Unconventional Family**

Michael remembered the last thing that Master Splinter told him before he left New York to head back to California. See, Master Splinter told Michael to act calm under pressure, keep their cool, and whenever something goes wrong that is unexpected, try tomake sure that things don't go really haywire.

Of course, with the situation as it is right now on the other hand...

"AHHHH! Get him off of me!" Mikey screamed as Michael had his arm wrenched behind his back.

"You idiot!" Michael screamed

"MIchael! You're gonna break his arm!" Leo yelled, trying to get Michael off of his brother.

"That's only because I can't get to his neck!" Michael screamed. Donnie and Leo finally broke up the little scrap that Mikey and Michael were having, and they managed to keep it separated.

"Okay. What are you going to say once she comes to?" April asked Michael. Michael sighed, ran a hand through his hair, and looked over at Miley, who was sound asleep on the couch in April's living room.

"The truth." Michael answered. "Thanks to Mikey here, there is no lie that I can tell that is going to make her forget what she saw here."

"I think you broke my arm." Mikey whined.

"I am going to do a lot worse if you don't shut your mouth." Michael said, rearing back his arm to show that he meant it.

"Calm down. Just sit back and think." Leo said, pulling Michael to the side. "Look, April is right, what are you going to tell her when she comes to?"

"I have no idea." Michael said. "I have no idea at all."

* * *

><p>After about a little while resting after she fainted, Miley started to come to. She began to stir, and tried to sit up when Michael rushed to her side.<p>

"Hey, Miley. How are you feeling?" Michael asked her.

"Fine. All things considering." Miley said. She looked over in the direction of the Turtles, and visibly flinched with fear.

"Calm down, they are family." Michael smiled at her. Michael then pointed at each one as he introduced them all. "That's Leonardo, Michaelangelo, Raphael, and Donatello."

Miley waved weakly at them then whispered in Michael's ear.

"Family? But they are Mutant Turtles." Miley whispered loudly to him.

"No, really? We're not deaf either." Raph said from across the room.

"Michael, how did you meet them?" Miley said.

"Well, I kind of ran into them." Michael said. "I was trying to find out what happened to my mom, and I sort of ran into them when I came back to New York a few years ago. I was raised by their father, and when I went to see their dad, I met them."

"See," Donnie spoke up, "My brothers and I were created by mysterious ooze called mutagen which mutates things."

"Mutates things, how?" Miley asked.

"Anyway." Leo answered. "We have seen this stuff in action personally, and it will mutate things in any way possible. What you turn into is kind of random."

"We were regular turtles at first, then we grew into teenagers." Donnie said.

"So, how do you guys run around the city, looking the way you do?" Miley asked.

"It's not as if we are monsters." Raph said. "To answer your question, we stick to the rooftops, and it also helps that we are only out at night, if at all."

"Speaking of nighttime, we better get back before Master Splinter deshells us." Leo said to his brothers and April.

"Do you really think Master Splinter would be angry with you guys for being out late? He seems like a calm character if you think about it." Michael asked him.

"Yeah, with a temper worse than Raph's." Mikey said.

"Hearing that, you better beat it before he gets really mad." Michael said. Leo gave a quick nod, and in a flash, the four Turtles were out the window, and heading home in the darkness.

* * *

><p>It was kind of funny, if you think about it. Miley wanted to know about his family in New York, but she really did not want to press it because she felt that something happened out here that was tragic and it made him leave for California. There were some answers that Miley had now, but that was not going to be it by a long shot. She knew there was something else here, but what?<p>

They were back at their hotel, and after the night that they had, or rather Miley had, she now knew about his family, but that raised a lot more questions than answers.

"Why didn't you tell me that you knew four Mutant Turtles?" Miley asked him.

"Honestly, you would not have believed me." Michael answered. "I contemplated telling you about it, but I figured that there was no chance on earth you would have thought that I was telling the truth."

"I heard them mention someone by the name of Master Splinter. Who is he, another turtle?" Miley asked him.

"No." Michael said.

"Well, who is he?" Miley pressed him.

"If he allows it, you will go and meet him." Michael said.

"Michael, just what happened that made you leave here and come to California?" Miley asked him. Michael sighed, and told her the truth.

"When I get the whole story, so will you." Michael said, giving her a smile.

All Miley could say, or do in this instance, was smile back, feeling glad that he finally trusted her to tell something at least.

* * *

><p><strong>AN: Okay, not to give too much away, but the next chapter is going to be about Michael, with help from the Turtles of course, getting to the bottom of his past, but first, Miley meets Master Splinter. Thanks, and enjoy.<strong>


	6. The Manhattan Project

**AN: In this chapter, Miley finally meets Master Splinter, and while they get aquainted with each other, the Turtles and Michael pay a visit to TCRI, and things sort of spiral from there.**

**Chapter Six: The Manhattan Project**

Michael and Miley were in their hotel room, watching TV late at night when he heard someone knocking on the front door. Michael slid off of the bed, and answered the front door, to be greeted by Donnie and Mikey.

"Nice to see you guys, but what's up?" Michael asked them.

"Listen, I was digging, and I found out something that you might be interested in knowing." Donnie said.

"What?" Michael asked them.

"Your mother was working on something at TCRI, but before we went and found out more, I figured that you might be of some help." Donnie said.

"Donnie doesn't know, from what I figured out." Mikey said under his breath. Donnie reached over and smacked Mikey hard before continuing.

"We want you to come with us while we figure this out." Donnie said.

"I would be glad to help you out, but where is Miley going to be while we do this?" Michael said.

"Take her to Master Splinter. She can hang out with him while we are doing our thing." Mikey said.

"Is he going to be cool with this?" Michael asked him.

"Sure." Donnie said. "I hope..."

"Okay, so when do we leave?" Michael asked them.

"Right now." Donnie said, pointing down at the Shellraiser, parked down in the middle of the parking lot of their hotel.

"Sweet. Let's do this." Michael said.

* * *

><p>It was a big surprise. Miley was really nervous about meeting Master Splinter, and she half expected him to be a turtle, like Leo, Donnie, Mikey, and Raph were. After trekking through the sewers to the lair, by trekking, I mean she was blindfolded, and led there, she finally arrived at the Turtles lair to meet their (and this is including Michael, mind you) father figure. To her genuine surprise, he was not a turtle. Of course, that would make too much sense. Michael calmly introduced Miley to Master Splinter, and the five of them soon left to go on their mission, while Miley stayed in the company of Master Splinter.<p>

"So, you are a rat." Miley said to Splinter.

"Yes, I am aware of that." Splinter said, chuckling a little under his breath.

This was getting to be an awkward conversation between the two of them, and Master Splinter was the one that broke that awkwardness.

"I take it that you want to know about my relationship between Michael and my sons." Splinter said.

"Of course." Miley said.

Master Splinter took a deep breath, and started.

"I found Michael wandering the streets while he was a young child." Master Splinter began. "It was winter, and really cold outside. It has alwaays amazed to this day that a child of that age managed to survive that long in the cold on his own. I brought him down here to the sewers, which I knew that he was not going to stay here forever, as I mananged to find some family of his out there in California, so once Michael got to be the right age, I sent him out there to meet his family."

"I remember that." Miley said. "I met him around that time that you mentioned. Master Splinter, I heard Michael mention this name, but who is the Shredder."

"A cold blooded killer." Master Splinter said, his tone taking a serious one. "One day, when I was still human, he attacked me and my wife. A blow that was meant for me hit my wife, and killed her. Ironically, when I found Michael, I thought about my wife, and knew immediately that Shredder was involved, but I could never prove it."

"I never saw Shredder, and after what you told me, I hope I never do." Miley said. "Master Splinter, what are the Turtles and Michael going to find at TCRI?"

"The truth. TCRI made the ooze that mutated me and my sons." Master Splinter said. "Whatever they are going to find, it is going to change Michael."

* * *

><p>Michael was surprised at how easy it was to get into TCRI headquarters. Sure, they had to be quiet, and get past security measures, but it was kind of easy. Of course, this being the Turtles we are talking about, it made sense that they were able to get into TCRI because this was not their first time that they were able to get in here. The five of them slowly made their way to the TCRI Archives, and once Donnie unlocked the door, they were able to get inside.<p>

"Alright, what are we looking for?" Leo asked.

"Anything with my mom's name on it." Michael said as the five of them spread out to search the room.

CRASH.

"MIKEY!" All four hissed in unison.

"Sorry!" Mikey apologized. After they made sure that they were not discovered, the five of them went back to searching the archives.

"Hey, look. Here's something with your mom's name on it." Raph said, from across the room. He handed a DVD in its plastic booklike case to Donnie and Michael.

"What is 'The Manhattan Project'?" Leo asked them.

"No idea. Let's watch it." Michael said.

Donnie went over to one of the vacant computer, and slipped the DVD carefully in the player on the computer. Soon enough, the player started on its own. The five of them gathered around as a blonde woman, similar to the way that Michael looked appeared on the screen.

_My name is Lori Ann Harris, and I am a scientist at TCRI in New York City. I am in charge of the Manhattan Project, a project that uses TCRI chemicles to alter human cells. I have a child named Michael that was terminally ill. I used the altering chemicles on Michael, and it is as though he is a new boy. I cannot believe that I may have found a way to maybe save terminally ill children, or maybe adults. I have to keep working on this to make sure that it is perfected._

There was a pause briefly, and then she appeared once again, the tone much different than when she appeared the first time.

_L-Listen, I do not know what might happen to me, or my son, but I need to leave this last video message. Charles Morris, the father of Michael, is working with Shredder and the Foot, and he had told them about the project I am in charge of, and now I am certain that my time is near its end. I don't know if you will ever get this message, Michael, but I hope that you will always know that I always loved you and proud that you were my son..._

The video cut off there. The four turtles stared at each other, and back at Michael. Michael took the DVD out of the computer, and put it back in its case.

"Michael, are you okay?" Leo asked putting a hand on his friend's shoulder.

"Fine. Let's get back, because I am sure that Miley is putting Splinter through the loops." Michael said, trying to laugh, but Leo could see that his friend was fighting back tears.

* * *

><p>Michael and the Turtles made their way back to the lair, and while the Turtles told Splinter what they found out at TCRI, Michael and Miley made their way back home. Miley could tell that there was something on his mind, as they walked back to their hotel, and he wanted to tell her what he found back there at TCRI.<p>

"Michael, what happened?" Miley asked in a soft tone of voice. Michael took a deep breath, and told her what happened.

"Shredder killed my mom." Michael said. "My dad sold us out to Shredder. Mom was working on 'The Manhattan Project', which I was the center of, and my dad was working with the Foot and Shredder. Shredder found my mom and killed her."

"Oh, Michael. I'm so sorry." Miley said, giving him a hug. Michael returned the hug, and they continued to walk on their way back to the hotel.

* * *

><p>They were a few feet from their hotel, but once they got to the street that their hotel on, Michael knew that they were not alone.<p>

"What's wrong?" Miley asked Michael, sensing the uneasyness in her friend. Before Michael could answer, a big menacing man appeared in front of them. He looked like he could kill the both of them very easily.

"Shredder." Michael said, hatefully. Shredder laughed proudly, and took a step towards them.

"Nice to meet you again, Michael, and I assumed that this is your girlfriend?" Shredder said, pointing towards Miley. Michael pulled Miley behind him, and Shredder laughed happily.

"What do you think you are going to do?" Shredder said, taking his hand, and knocking Michael backwards, nearly knocking him unconscious. Miley wanted to run to check on her friend, but Shredder appeared in front of her, a big metal claw appearing above her.

"Now to give you a taste of what I did to his mother." Shredder said in an ice cold tone.

Miley braced herself for what was a killing blow, and saw Shredder swing at her, but when the blow never came, she opened her eyes to see that Michael appeared in front of her, taking the hit that was meant for her. Michael shakingly looked back at her, and she saw tears in his eyes, as he fell over, dead.

Miley turned to run, but was surrounded by Footbots. Her arms were bounded behind her back as she looked Shredder in his eyes.

"Please, don't kill me..." Miley pleaded.

"I won't, not now at least." Shredder said. Shredder laughed as his Footbots took Miley away.

* * *

><p><strong>AN: The final chapters are next, and more is going to be revealed next time.<strong>


	7. Showdown Part One

**AN: After the events of the last chapter, we are going to see just what the results of Shredder's attack is, and what else is in store for everyone involved. Love surprises, anyone? Well, there is going to be one for Shredder and the Foot, as well.**

**Chapter Seven: Showdown Part One**

As a leader, Leonardo had certain suspicions about the city when certain things were happening. This being New York City, mind you, that feeling of worry was an almost constant little nagging that he had. This little worry that he was currently experiencing was really weighing on his mind. See, it was not more than a few hours earlier that his brothers, and Michael broke into TCRI to see just what his mother worked on before she died. All five of them were soon caught up with Michael's plight, as they were informed that _The Manhattan Project, _the project that Michael's mom was working on, was also sought out by the Foot, and that alone led to the death of Michael's mother, who was sold out by his very own father. Leo wondered if Michael was alright, because the four Turtles did not hear from him at all since they left TCRI. To be fair, the time in which the five of them left TCRI, was only a few hours ago mind you. Still, Leo was a little bit concerned that Michael was silent since that time.

Leo stood in the doorway of the lair, with Mikey on the floor in front of the TV with his eyes glued to the television watching some new cartoon. Leo was about to join him when he got a message on his T-Phone. He took a real small sigh of relief when he saw that it was Michael sending him a text. Then it was the nature of the text that caused Leo's expression and demeanor to change.

_Shredder attacked. We need help..._

Upon reading that message, Leo ran into the main area of the lair, and his four brothers looked to him in mild shock due to the expression on his face.

"Guys! Michael and Miley were attacked by the Foot! Come on, let's go!" Leo yelled.

The four turtles ran to the Shellraiser, and drove out into the New York darkness.

* * *

><p>With Donnie being able to triangulate the signal of Michael's T-Phone, the Turtles quickly were able to find the location of where Michael's message came from. The Shellraiser came to a screeching halt, and the four brothers quickly hopped out to quickly find their friends.<p>

"Do you see them?" Raph asked, looking around.

"I don't see a single sign of them." Donnie said, looking around.

"Maybe the signal came from a larger place." Mikey said, taking a look around.

"No, this is the only area where the signal came from, the exact area." Donnie said.

"Guys, I found him..." Leo said, his voice just over a whisper. Mikey, Donnie, and Raph gathered around Leo, who was kneeling in front of Michael. The four just stared at what Shredder had done to their friend. It was obvious that Shredder was ruthless, but seeing what they did to their friend was a little hard for them to take at the moment. There was no way that Michael was alive, at least from the way that they were looking at it.

It looked as though he was wearing a red shirt, rather than the white one that they had seen him in a few hours earlier.

"Man, what happened to him?" Mikey asked.

"Shredder, that's what happened to him." Leo said. Leo kneeled before their friend, and placed a hand on his forehead.

"What are we going to do?" Donnie asked.

"We take care of Michael, then we find Miley. That's what we are going to do." Leo said.

Leo was about to go when he heard very faint breathing. He turned his head to see the chest of Michael slowly, but surely rising. His breathing was labored, but it was a good sigh of relief to the Turtles that he was alive, but they better do what they can to make sure that he stays that way.

"Quick, get him into the Shellraiser! We have to get him back to the lair, quickly!" Leo said. The four Turtles quickly, and carefully gathered up their friend, and put him into the Shellraiser, and raced back to the lair.

* * *

><p>It was funny in a way. Not funny "ha ha", but funny "strange". See, the Turtles got Michael back to the lair quickly and carefully enough as to not hurt him, but it was weird that as they were heading back, something strange was going on with him. Donnie quickly went to work on Michael, and Leo, Raph, Mikey, and Master Splinter were waiting outside the room that Donnie was in, working on Michael.<p>

Leo, Raph, Mikey, and Master Splinter were anxiously waiting outside, waiting for word on Michael's condition, then Donnie stepped outside, a confused look on his face.

"Guys, we have a situation." Donnie said.

"What? Did Michael die?" Leo asked, concern obvious in his voice.

"No, he getting better." Donnie said, confused.

"Wait, isn't that a good thing?" Mikey asked.

"It is, but something is just really strange about it." Donnie said.

"Just how is it strange?" Raph asked.

"See," Donnie took a deep breath before continuing, "as I was examining Michael's wound, I sort of noticed that it was healing on his own. I was curious as to why it was doing that, then I remembered _The Manhattan Project _that his mom was working on. I guessed that somehow was contributing to this."

"What about the attack by Shredder?" Leo asked.

"This is the Shredder we are talking about." Donnie said. "With what we know about the Shredder, we all know that he won't hesitate to kill, and the fact that Michael isn't dead, means that we are not dealing with some random human here, no matter what he is."

"Why would Shredder kidnap Miley though?" Mikey asked.

"Honest guess, to get to Michael, but I have no idea why the Shredder would want something from Michael. The stuff we got from TCRI doesn't tell us anything about _The Manhattan Project._" Leo said.

"Does the Shredder know that?" Raph asked.

"I guess not, but if push come to shove, we could use that to our advantage." Leo said.

* * *

><p>Master Splinter and the rest of the Turtles stood over Michael, and just stared at him. They stared at him as if he was dead, but for some strange reason, he was recovering, from a mortal wound from the Shredder. They had to go and find Miley before something really bad happened to her, but what was the chance that had already happened?<p>

All of a sudden, Michael began to stir, and sit up. Leo rushed to his side, and helped his friend sit up.

"Easy there, are you all right?" Leo asked him.

"Fine, my ribs hurt like hell." Michael said.

"Young Michael." Master Splinter said, getting his attention. "What happened earlier tonight?"

"We were heading back to the hotel, and Shredder jumped us." Michael began. "Then when he was about to attack her, I jumped in front of her, and took the hit. I thought that I was dead."

"The blow from Shredder should have killed you, but it didn't. Why?" Leo asked.

"I have no idea." Michael said. He swung his legs off of the table, wincing against the pain in his midsection. He looked around for something, or rather someone.

"Guys, where's Miley?" Michael asked the five of them.

The Turtles shared a look with each other, and Michael immediately knew that their answer, if there was one, was not going to be a good one.

"Guys, where's Miley?" Michael asked, now sounding panicked.

It was a moment before they answered, but when the answer came, it came from Leo.

"Michael, she's gone."

* * *

><p><strong>AN: In the next chapter, Shredder makes his demands, and a confrontation with the Foot is in the air. Thanks for reading, and stay tuned for more!<strong>


	8. Showdown Part Two

**AN: Miley has been captured by the Foot, and in the process, Michael was injured by the Shredder. The Turtles, Splinter, and Michael have no ideas what their demands are, but that is about to change...**

**Chapter Eight: Showdown Part Two**

It took a moment to register what Leo had just told him. Miley was gone, but just exactly was she saying? Michael was immediately thinking the worse. Before Michael lost consciousness, he knew that Shredder was involved. Michael was still thinking the worse, but Leo spoke once again.

"The Foot has her." Leo said. Michael let out a small breath. He knew that to an unknown extent that Miley was alright, but that does not mean that this is over by a long shot.

"What exactly happened?" Michael asked them.

"We found you, brought you back here, and began to patch you up." Donnie said, speaking up. Then the brainy turtle continued. "You managed to survive an encounter with Shredder, but what gets me is how you are healing from the encounter.

"What are you talking about? How does this have anything to do with why Shredder took Miley?" Michael asked, getting somewhat impatient.

"I'm getting to that." Donnie said. "You are healing quickly, and naturally, which means that most likely Shredder took Miley in an attempt to get information on The Manhattan Project, or the work that your mom did on the project."

"Does Shredder know that we went into TCRI somehow?" Leo asked.

"Probably. That could be how Shredder knows about The Manhattan Project still being around, and some stuff about Michael." Donnie said.

It was silent for a few moments, then Michael had a really frightening thought.

"Guys, what do you think Shredder is doing to Miley?" Michael asked them.

The Turtles and Shredder knew all too well, and this was from personal experience first hand of course, that Shredder was capable of really terrible things. What Michael experienced, was rather light. They did not tell him that, of course. They knew that Michael was really worrying about Miley, and that his mind was racing with worry.

Leo crossed the room, and placed a comforting hand on his shoulder.

"Don't worry, Michael. We are going to find her." Leo said, giving him a weak smile.

Leo's words were somewhat comforting, but with Miley being in the hands of the Foot, he knew that he was not going to be able to rest, if he was able to at all.

* * *

><p>The last thing she remembered was Michael being struck down by the Shredder, and then being brought here by these ninjas, or whatever they were. They blindfolded her, tied her hands behind her back, and she could feel these guys bringing her to an unknown location. From what she could tell, once they arrived at their headquarters, they sat her down somewhere, and after a few minutes, they picked her up, and dragged her somewhere. They sat her down, and yanked the blindfold off of her. There she saw the same man who struck down her best friend.<p>

"Greetings Miley." Shredder said. Miley looked at him, and felt hatred growing for him for some strange reason. "We met earlier, when I struck down your boyfriend."

"He's not my boyfriend." Miley said. That pissed Shredder off, because before she knew it, Shredder backhanded her, and Miley tasted the iron of blood in her mouth.

"Don't you dare interrupt me!" Shredder screamed, Miley snapped her head back in the direction of Shredder's face. She spat some of the blood in her mouth in his direction, and he laughed in the attempt that she made of defiance.

"What do you want?" Miley asked him.

"Getting right to the point, huh? Well, you are right, there is no real need for formalities now, huh?" Shredder said, laughing evilly.

Miley now hated this guy, and she only knew him for a matter of minutes. Then Shredder continued.

"I want you to know that your friend is alive." Shredder said, looking at Miley's expression change to one of someone having a faint glimmer of hope.

"Really? How?" Miley asked.

"Because, he is a freak, just like his Turtle friends." Shredder said. "I am after something that his mother was working on, and he has that information. I know that he would not hand it over voluntarily, but now that I have you, I know that he will do anything to get you back."

"I hope he tears your head off." Miley said, loudly enough so that he could have heard her. Shredder slowly nodded his head, and walked to where she was standing. With one of his bare hands, he struck Miley in the side of her head, knocking her unconscious.

"Don't worry. When I get my hands on the Turtles and your boyfriend, I intend to do much worse." Shredder said.

* * *

><p>It was difficult for Michael to sit there, and wait for any type of news about what happened to Miley. Leo and Raph went upside to look around for any type of sign, or anything for that matter, to see what they could find. Donnie and Mikey tried to lift his spirits by letting him know that Miley was going to be fine, but Michael knew that in the back of his mind, she was less likely to even be alive.<p>

It was slow going. Then all of a sudden, Leo and Raph returned, with rather stoic looks on their faces.

"Well, what did you find?" Michael asked them.

"This." Leo said. He handed a DVD to Michael. Michael looked at the DVD, which had the Foot insignia on the front of it, and back at Leo and Raph.

"Where did you find this?" Michael asked them.

"At your hotel room." Raph answered. "We went there to see if anything was out of place, and we found that on the bed."

"This is going to show what Shredder wants from you, most likely." Leo said.

"Well, let's see what is going on." Michael said. He put the DVD in the portable DVD player. The Turtles and Michael gathered around the screen, with eager anticipation. After a few moments, Shredder's mask soon appeared onscreen.

_Greetings, Michael. Turtles. I have your friend Miley in my possession. In exchange for her safe return, I want info on the Manhattan Project. Meet me at the top of the Empire State Building tonight at Midnight. If you do not show up, Miley will end up just like your mother. See you soon._

Short, brief, and to the point. Shredder knew what he wanted, but the thing was, was that there was nothing to give. The Manhattan Project information was never found, even after Michael and the Turtles went to TCRI. Whatever they had, was not enough, and they knew it.

* * *

><p>It was about an hour until Shredder's deadline, and while the other Turtles were preparing for this in their own way, Leo watched as Michael was getting dressed on his own. Michael strained getting a shirt on over his head, and once Michael was fully dressed, he turned to Leo.<p>

"Leo, what can I expect from a meeting with Shredder?" Michael asked. Michael's voice was shaky, and Leo's answer was not going to make him feel any better.

"Expect anything, Michael." Leo said. "Expect anything."

Leo's words did not make him better, but at least his words were honest.

"Come on. We better go." Leo told Michael.

Michael had no idea what was waiting for him, nor did the Turtles themselves.

* * *

><p><strong>AN: Next time, the Turtles and Michael confront Shredder and the Foot, and a surprise is in store for all of them.<strong>


End file.
